This is always tough to do (as it’s like asking someone with a bunch of kids which ones are his favorites), but here’s a sampling. See our Papers page for more details and the paper #’s I’m refering to. Google has a list of our most cited papers: http://scholar.google.com/citations?user=cWe_xpUAAAAJ
de novo simulations of protein folding with quantitative agreement with experiment
While paper #1 (Shirts and Pande, Science, 2000) got the ball rolling, paper #8 (Snow et al, Nature, 2002) was important since it was the first time that experiment and simulation could really match in this sort of quantitative fashion. It was a test of many aspects of FAH and turned out quite well quantitatively.
Paper #17 is another good example of this, where we compared to multiple experimental methods.
This early work has been followed up by numerous works after to better understand folding, including folding in vitro (53, 49, 45, 42, 37, 35, 33, 24, 23, 22, 19, etc) and models of in vivo (#50, #36).
New drug design methodology
We have also been pushing the boundaries of what can do with computational drug design (method in paper #29, results in paper #31 and #43, where we showed that our methods were very accurate, for a target of pharmaceutical relevance)
New methodology to simulate folding on distributed networks
We have also had major efforts to further enhance our methods to push FAH to do more and more. This includes papers 54, 49, 46, 40, 32, 27, 26, 19, etc.
Applications to disease
Most of the exciting work is still under peer review (I think it always feels like that for scientists, as it takes ~1 year for review/publication), however some highlights that are already out include our work on cancer (papers #39 and #20) and lipid fusion, relevant for viral infection (papers #41, #47, #51)